| GeneSetCollection-methods {GSEABase} | R Documentation |
Methods to construct GeneSetCollection instances
Description
Use GeneSetCollection to construct a collection of gene sets
from GeneSet arguments, or a list of
GeneSets.
Usage
GeneSetCollection(object, ..., idType, setType)
Arguments
object |
An argument determining how the gene set collection will
be created, as described in the methods section. |
... |
Additional arugments for gene set collection construction,
as described below. |
idType |
An argument of class
GeneIdentifierType, used to
indicate how the geneIds will be represented. |
setType |
An argument of class
CollectionType, used to indicate how the
collection is created. |
Methods
-
signature(object = "GeneSet",idType="missing", setType="missing")
- Construct a gene set collection from one or more
GeneSet
arugments.
-
signature(object = "list", idType="missing", setType="missing")
- Construct a gene set collection from a list of
GeneSets.
-
signature(object="missing", idType="AnnotationIdentifier", setType="CollectionType"),
signature(object="missing", idType="AnnotationIdentifier", setType="CollectionIdType")
- Construct a gene set collection of
CollectionType entities (e.g., pathways for
KEGGCollection, protein families for PfamCollection)
implied by the map found in annotation(idType). If setType is a
CollectionIdType and length(ids(setType))>0, the
gene set collection is filtered to contain only those sets implied
by the ids.
-
signature(object="character", idType="AnnotationIdentifier", setType="CollectionType"),
signature(object="character", idType="AnnotationIdentifier", setType="CollectionIdType")
- Construct a gene set collection of
CollectionType entities (e.g., pathways for
KEGGCollection, protein families for PfamCollection)
implied by the map found in annotation(idType). Use only
those identifiers in object. If setType is a
CollectionIdType and length(ids(setType))>0, the
gene set collection is filtered to contain only those sets implied
by the ids.
-
signature(object="ExpressionSet", idType="missing", setType="CollectionType"),
signature(object="ExpressionSet", idType="missing", setType="CollectionIdType")
- Construct a gene set collection using the
annotation and
featureNames of object to identify elements for
CollectionType gene sets (e.g., pathways for
KEGGCollection, protein families for PfamCollection)
implied by object. The gene set
collection contains only those AnnotationIdentifiers found
in featureNames(object); if setType is a
CollectionIdType and length(ids(setType))>0, the
gene set collection is further filtered to contain only those sets
implied by the ids.
-
signature(object="ExpressionSet", idType="missing", setType="GOCollection")
- Construct a gene set collection using the
annotation and
featureNames of object to identify
GO pathways implied by object. The map between
featureNames and GO pathway identifiers is derived
from the GO2PROBE table of the annotation
package of object. The gene set collection contains only
those AnnotationIdentifiers found in
featureNames(object). The evidenceCode of
GOCollection can be used to restrict the pathways seleted to
those with matching evidence codes.
-
signature(object="missing", idType="AnnotationIdentifier", setType="GOCollection")
- Construct a gene set collection containing all GO pathways
referenced in the annotation package of
idType. See the
signature(object="ExpressionSet", idType="missing",
setType="GOCollection") method for details.
See Also
GeneSetCollection
Examples
gs1 <- GeneSet(setName="set1", setIdentifier="101")
gs2 <- GeneSet(setName="set2", setIdentifier="102")
## construct from indivdiual elements...
gsc <- GeneSetCollection(gs1, gs2)
## or from a list
gsc <- GeneSetCollection(list(gs1, gs2))
## set names must be unique
try(GeneSetCollection(gs1, gs1))
data(sample.ExpressionSet)
gsc <- GeneSetCollection(sample.ExpressionSet[200:250],
setType = GOCollection())
[Package
GSEABase version 1.4.0
Index]